title: WT_90FR

city: Umeå

first: Stephan

last: Wenkel

address: Parallellvägen 21

country: Sweden

institute: Umeå Plant Science Center

data_processing:
The isoseq3 pipeline provided by PacBio was run in an Ubuntu environment, including the lima, refine and cluster steps.
The obtained HQ reads after the clustering step were mapped to the TAIR10 Arabidopsis genome using minimap on Galaxy. The minipam.bam files were obtained.
The reads files generated before running the clustering step of the isoseq3 pipeline were mapped to the TAIR10 Arabidopsis genome using minimap on Galaxy. The Mapped_ISOSEQRefinedStep.bam files were obtained.
Assembly: TAIR10
Supplementary files format and content: The clustered.hq.fasta.gz files are the output of the isoseq3 pipeline, after the clustering step and the conversion to a fasta format. They include high quality clustered reads. These files were used to prove the presence of the alternative transcript of interest.
Library strategy: Iso-seq

organism: Arabidopsis thaliana

source_name: Whole 12 days old seedlings

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA Kit (Sigma)
Input RNA quality control, cDNA synthesis, 3 cDNA amplification, Repair and A-tailing, Adapter ligation, Nuclease treatment.

value: Whole 12 days old seedlings

value: Wild-type seedlings

value: WT

value: 90 minutes FR enriched light


title: WT_WL

status: Public on May 22 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: White light


title: YAP5SA3

city: WORCESTER

first: Susu

last: Guo

state: MA

address: 7 Pocono Road

country: USA

institute: UMASS Chan Medical School

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: RNA_seq_fpkm.xlsx

organism: Homo sapiens

growth_protocol: DMEM with 10% FBS

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HEK293T cells were transient transfected with pcDNA3.1, VGLL2-NCOA2, TEAD1-NCOA2 or YAP5SA palsmids.

value: Human embryonic kidney cells

value: YAP5SA overexpression

value: transient transfection YAP5SA


title: Hi-C of Bos taurus DNA Zoo Sample6770, DIY sirloin jerky in toaster oven, dehydrated for 1h

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
HIC16973.hic
HIC16973_30.hic

library_source: genomic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

molecule: genomic DNA

organism: Bos taurus

source_name: sirloin

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: sirloin


title: Adipose Tissue, HIV+NonDM, 1115

city: Nashville

first: Samuel

last: Bailin

address: 1161 21st Avenue South, MCN A-2200

institute: Vanderbilt Universit Medical Center

data_processing:
Samples were sequences in two batches on the Illumina NovaSeq 6000 platform using paired-end sequencing (2 x 150 pb)
Read quality was assessed and adapter read-through sequences were removed using fastp
Reads were mapped to the Human GENCODE release 34 hg38 using STAR v2.7.3a
FeatureCounts was used to assign reads to features using GENCODE v34 annotation
Assembly: GENCODE release 34 GRCh38
Supplementary files format and content: text file with raw counts from featureCounts

molecule: polyA RNA

source_name: subcutaneous adipose tissue

extract_protocol:
Total RNA was extracted from subcutaneous adipose tissue using Qiagen RNeasy Lipid Tissue Kit after mechanical lysis.
cDNA libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kits

value: subcutaneous adipose tissue

tag: Sex

value: Male

tag: disease state

value: HIV+ non-diabetic


title: Adipose Tissue, HIV+preDM, 1114

value: HIV+ prediabetic


title: Hi-C of Bos taurus DNA Zoo Sample6769, Bovine heart, ~48hhpm, +68h @RT

description:
HIC16984.hic
HIC16984_30.hic

source_name: heart

value: heart

value: Bovine heart, ~48hhpm, +68h @RT


title: Adipose Tissue, HIV+preDM, 1116


title: T2

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

data_processing:
First, the adaptor sequences and polyA sequences were trimmed and filtered out using fastp (ver 0.23.2)
RNAseq reads were aligned to the human reference genome (hg38) using the STAR (v2.7.9) software.
The R Subread package with the featureCount function generated RNA-seq raw counts for quantification (ver2.0.3).
Read count were normalized using RPKM for QC.
Genes expressed at very low levels, with maximum expression <0.1 RPKM from all samples, were excluded from downstream differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count for each Sample

extract_protocol:
Treated Samples were purified using the RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared with KAPA mRNA HyperPrep Kit following manufacturer's protocols.

value: SCLC

value: Teriflunomide


title: Hi-C of Bos taurus DNA Zoo Sample6769, Bovine heart, ~48hpm, +24h @RT, rep3

description:
HIC16971+HIC16972+HIC16983.hic
HIC16971+HIC16972+HIC16983_30.hic

value: Bovine heart, ~48hpm, +24h @RT, rep3


title: Control3

value: Wild Type

value: transient transfection pcDNA3.1


title: Adipose Tissue, HIV+NonDM, 1112


title: VN3

value: VGLL2-NCOA2 overexpression

value: transient transfection VGLL2-NCOA2


title: T3


title: Hi-C of Bos taurus DNA Zoo Sample6769, Bovine heart, ~48hpm, +24h @RT, rep2

value: Bovine heart, ~48hpm, +24h @RT, rep2


title: TN3

value: Human embryonic kidney cells

value: TEAD1-NCOA2 overexpression

value: transient transfection TEAD1-NCOA2


title: Adipose Tissue, HIV+NonDM, 1111

value: subcutaneous adipose tissue


title: WT_45FR

value: Whole 12 days old seedlings

value: Wild-type seedlings

value: WT

value: 45 minutes FR-enriched light


title: C1

value: Control


title: T1

value: SCLC


title: Hi-C of Bos taurus DNA Zoo Sample6769, Bovine heart, ~48hpm, +24h @RT, rep1

value: heart

value: Bovine heart, ~48hpm, +24h @RT, rep1


title: C3


title: C2


title: Hi-C of Bos taurus DNA Zoo Sample6769, Bovine heart, ~48hpm, rep3

description:
HIC16969+HIC16970+HIC16981.hic
HIC16969+HIC16970+HIC16981_30.hic

value: Bovine heart, ~48hpm, rep3


title: Adipose Tissue, HIV+NonDM, 1110

value: Male

value: HIV+ non-diabetic


title: YAP5SA2

value: YAP5SA overexpression

value: transient transfection YAP5SA


title: Hi-C of Bos taurus DNA Zoo Sample6769, Bovine heart, ~48hpm, rep2

value: Bovine heart, ~48hpm, rep2


title: VN2

value: Human embryonic kidney cells

value: VGLL2-NCOA2 overexpression

value: transient transfection VGLL2-NCOA2


title: Adipose Tissue, HIV+NonDM, 1109

value: subcutaneous adipose tissue

value: Female


title: Control2

value: Wild Type

value: transient transfection pcDNA3.1


title: Adipose Tissue, HIV+NonDM, 1113


title: Hi-C of Bos taurus DNA Zoo Sample6769, Bovine heart, ~48hpm, rep1

value: Bovine heart, ~48hpm, rep1


title: VFB_POP#12

city: Scottsdale

first: Xianfeng

last: Chen

state: AZ

address: 13400 E Shea Blvd

institute: Mayo Clinic

data_processing:
processed with Mayo Clinic internal secondary pipeline MAPRseq. Basically reads QC by cutadapt, aligned by BWA, mutation called by GATK
FDR <0.05) to identify differentially expressed genes (DEG).
Assembly: HG38
Supplementary files format and content: gene expression profiling (tab-delimited)
Supplementary files format and content: differential gene expression (tab-delimited)

source_name: Vaginal excised subepithelum

growth_protocol: Both type of cells (adipose derived stem cells and vaginal fibrobalsts) were expanded in clinically relevant advanced MEM medium (ThermoFisher) supplemented with 5% human platelet lysate (hPL) (PLTMax®, Mill Creek Life Sciences, Rochester, MN), 2U/ml heparin, and 2mM GlutaMAX™ and passaged 2-3 times.

extract_protocol:
Confluent ASCs and VFBs cultures were harvested in TRIzol (ThermoFisher). RNA was extracted with Direct-zol RNA kit (Zymo Research). 200 ng of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq mRNA Protocol following manufacturer’s protocol.

value: Vaginal excised subepithelum

value: primary vaginal fibroblasts (VFB or VFBs)

value: serum free expansion medium supplemented with human Platelet Lysate (hPL)

tag: time

value: 9-14 days

tag: density of_cultures_cells

value: confluency

tag: diseases state

value: pelvic organ prolapse (POP)


title: VFB_POP#11


title: Adipose Tissue, HIV+NonDM, 1108

value: Male

value: HIV+ non-diabetic


title: VFB_POP#10


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, blasted with shotgun

description:
HIC17083.hic
HIC17083_30.hic

source_name: liver

value: liver


title: YAP5SA1

value: Human embryonic kidney cells

value: YAP5SA overexpression

value: transient transfection YAP5SA


title: Adipose Tissue, HIV+NonDM, 1107

value: subcutaneous adipose tissue


title: TN1

value: TEAD1-NCOA2 overexpression

value: transient transfection TEAD1-NCOA2


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, hit with a fastball

description:
HIC17082.hic
HIC17082_30.hic

value: Freeze-dried liver, hit with a fastball


title: VFB_POP#9


title: Adipose Tissue, HIV+NonDM, 1106


title: VFB_POP#8


title: TN2


title: VN1

value: VGLL2-NCOA2 overexpression

value: transient transfection VGLL2-NCOA2


title: VFB_POP#7

value: Vaginal excised subepithelum

value: primary vaginal fibroblasts (VFB or VFBs)


title: Adipose Tissue, HIV+preDM, 1105

value: HIV+ prediabetic


title: Adipose Tissue, HIV+NonDM, 1103


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, rehydrated in lemon juice for 1h

description:
HIC17077.hic
HIC17077_30.hic


title: Control1

value: Wild Type

value: transient transfection pcDNA3.1


title: VFB_Ctrl#6

value: serum free expansion medium supplemented with human Platelet Lysate (hPL)

value: 9-14 days

value: confluency

value: controls - without pelvic organ prolapse (CTRL)


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, rehydrated in warm water for 1h

description:
HIC17076.hic
HIC17076_30.hic

value: liver


title: VFB_Ctrl#5


title: Adipose Tissue, HIV+NonDM, 1102

value: Male

value: HIV+ non-diabetic


title: Adipose Tissue, HIV+NonDM, 1101

value: subcutaneous adipose tissue


title: VFB_Ctrl#4


title: VFB_Ctrl#3


title: VFB_Ctrl#2


title: F_1_APLNrKO_ML233_24h_1

city: Portland

first: Thomas

middle: Dexter

last: Morse

state: ME

address: 154 New Island Ave

institute: MDIBL

data_processing:
The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection.
Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. At the same time, Q20, Q30 and GC content were calculated
Paired-end clean reads were aligned to the reference genome GRCz11 (Danio rerio)  using Hisat2 v2.0.5 < hisat2 -x reference_genome -p 4 --dta -t --phred33  -1 sample_1.clean.fq.gz -2 sample_2.clean.fq.gz --un-conc-gz sample.unmap.fq.gz 2> sample_align.log >
Mapped reads of each sample were assembled by StringTie [3](v1.3.3b) in a reference-based approach < stringtie sample.bam -p 4 -G genome.gtf -o sample.gtf --rf >
FeatureCounts [4] v1.5.0-p3 was used to count the reads numbers mapped to each gene. < featureCounts -T 4 -F GTF -t exon -g gene_id -s 2 -Q 10 -C -B -p -a genome.gtf -o feature_count.xls sample.bam >
Differential Expression Analysis was performed with the MDIBL Bioinformatics Core’s DESeq2 R script R version 4.3.2 and DESeq2 version 1.42.1. (parameters are contained in the report file: ML233_Simple_Base_Pairwise.html )
PCA Clustering was resolved using the R package PCAtools version 2.14.0
Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler version 4.10.1
Assembly: GRCz11 (Danio rerio) reference genome obtained from Ensembl
Supplementary files format and content: gene counts

organism: Danio rerio

source_name: embryo

growth_protocol: Zebrafish were aplnr(a/b) mutants derived from the AB strain, and wildtype controls derived from the same grandparents. Husbandry and procedures were as described previously. All animal procedures were approved by the Institutional Animal Care and Use Committee of the MDI Biological Laboratory, and all methods were performed in accordance with the relevant guidelines and regulations. To generate tyrosinase, apelin, apelin receptor a, and apelin receptor b mutants, we used tracrRNA and crRNA (IDT) to form functional gRNA duplexes targeting the ORF (apln: 5’-GAATGTGAAGATCTTGACGC-3’, aplnra: 5’-TGGGTGTGACTACTCGGAGT-3’ and aplnrb: 5’- CTTGCAGAGTGCCACGCCAA-3’). Co-injection of these gRNAs with the Cas-9 protein (IDT) resulted in indels in the apln, aplnra, or aplnrb gene coding sequences, identified by Sanger sequencing and analyzed with ICE software (Synthego) in F0 injected embryos. F0 carriers for mutations in the apelin locus in the germline were identified by sequencing the alleles on the clutches, and were then outcrossed to obtain F1 heterozygous mutants. F2 apelin homozygous mutants were also identified by sequencing. The apelin mutant harbor a 26-bp insertion leading to a stop codon at position 18 of the peptide.

extract_protocol:
Embryos were homogenized in Trizol solution (Invitrogen) and total RNA was purified using chloroform (Fischer) and then isopropanol (Fischer). RNA (1 μg) was reverse-transcribed using an oligo-dT primer and RevertAid kit (Thermo-Scientific). Total RNA samples for bulkRNAseq analysis were prepared with ~50 embryos/sample. Each experimental condition has been performed using biological quadruplicates to ensure reproducibility. Trizol (Invitrogen) was used to homogenize cellular extracts with the TissueLyzer (Qiagen). RNA purification was performed as described above.
RNA was quantified and sent to Novogene  for Illumina library preparation and paired-end sequencing.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesizedusing random hexamer primers, followed by the second strand cDNAsynthesis using dUTP.

value: embryo

value: KO

tag: developmental stage

value: 3 dpf embryo

tag: mdibl id

tag: conc um

tag: sequence count


title: F_2_APLNrKO_ML233_24h_2


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, dipped in LqN2

description:
HIC17029.hic
HIC17029_30.hic

value: Freeze-dried liver, dipped in LqN2


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, microwaved for 6min

description:
HIC17081.hic
HIC17081_30.hic

value: Freeze-dried liver, microwaved for 6min


title: scATACseq_CD34+_DONtreatment_24h_multipledonors

city: Paris

first: Laëtitia

last: RACINE

address: 27 rue de Chaligny

country: France

institute: EPHE

description: 10X scATACseq

data_processing:
Demultiplexing + Matrix generation with Cellranger (v6pipeline version cellranger-atac-2.0.0)
R (version 4.2,1) & Seurat (version 4.1.3) & Signac (version 1.9.0) & ggplot2 (version 3.4.2) & org.Hs.eg.db (version 3.16.0) & clusterProfiler (version 4.6.2)
Filters : 200 peaks detected per cell, nucleosome signal <2, blacklist ratio <0.05, TSS enrichment >2, 3000>number of fragments overlapping peaks> 50 000
Assembly: hg38 (GRCh38)
Supplementary files format and content: filtered_peak_bc_matrix.h5 files contain filtered peak barcode matrix with detected cellular barcodes
Supplementary files format and content: fragments.tsv.gz files contain chromosome, barcode, start and end position of each peak
Supplementary files format and content: singlecell.csv files contain QC per cellular barcode

source_name: umbilical cord blood

growth_protocol: CD34+ cells were purified from human healthy cord blood with a two-step immunomagnetic beads protocol and were then frozen in a cryopreservation medium. After thawing, CD34+ cells were cultured in a 96-well plate in a humidified 5% CO2 incubator at 37°C. Cells were grown in prestimulation medium made of X-Vivo (Lonza) supplemented with penicillin/streptomycin (respectively 100U/mL and 100µg/mL - Gibco, Thermo Scientific), 50 ng/ml h-FLT3, 25 ng/ml h-SCF, 25 ng/ml h-TPO, 10 ng/ml h-IL3 (Miltenyi) final concentration.

extract_protocol:
High viability percentage was obtained using a Dead Cell Removal kit (Miltenyi). scATACseq was then performed as described in the 10X Genomics protocol with Chromium Next GEM Single Cell ATAC-seq Kit v1.1. 15 000 nuclei were isolated and loaded on the chip to obtain around 4000-6000 nuclei encapsidated in GEM.
Library was prepared following the 10X Genomics protocol, controled with Qubit quantification and sequenced on a Novaseq6000.

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium with or without metabolic inhibitor (2-DG, DON or AOA) until lysis was performed. Cells were collected and lysed after 24h of cytokine stimulation.

value: umbilical cord blood

value: CD34+ cells

value: Healthy

value: 2.5uM DON


title: scATACseq_CD34+_2DGtreatment_24h_multipledonors

description: 10X scATACseq

value: 1mM 2-DG


title: VFB_Ctrl#1

value: Vaginal excised subepithelum

value: primary vaginal fibroblasts (VFB or VFBs)

value: serum free expansion medium supplemented with human Platelet Lysate (hPL)

value: 9-14 days


title: E_3_APLNrKO_ML233_3h_3


title: scATACseq_CD34+_Notreatment_24h_multipledonors

description: 10X scATACseq

value: Untreated


title: F_4_APLNrKO_ML233_24h_4


title: E_2_APLNrKO_ML233_3h_2


title: AMSC_POP#11

source_name: subcutaneous abdominal lipoaspirate

value: subcutaneous abdominal lipoaspirate

value: primary adipose derived stromal/stem cells (AMSC or ASC)

value: confluency

value: pelvic organ prolapse (POP)


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, heated in a toaster oven for 1h

description:
HIC16977.hic
HIC16977_30.hic

value: liver


title: E_1_APLNrKO_ML233_3h_1

value: embryo

value: KO

value: 3 dpf embryo


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, 11mo @RT, rep3

description:
HIC17075.hic
HIC17075_30.hic

value: Freeze-dried liver, 11mo @RT, rep3


title: F_3_APLNrKO_ML233_24h_3


title: AMSC_POP#12


title: AMSC_POP#10


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, 11mo @RT, rep2

description:
HIC17072.hic
HIC17072_30.hic

value: Freeze-dried liver, 11mo @RT, rep2


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, 7mo @RT, rep2

description:
HIC16917.hic
HIC16917_30.hic

value: Freeze-dried liver, 7mo @RT, rep2


title: scATACseq_CD34+_AOAtreatment_24h_multipledonors

description: 10X scATACseq

value: umbilical cord blood

value: CD34+ cells

value: Healthy

value: 1.9mM AOA


title: HEL cells, LRCherry2.1-sgDCAF15#2, rep2

city: Philadelphia

first: Luca

last: Busino

state: Pennsylvania

address: 421 Curie Boulevard

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Reads were mapped and analyzed with a bioinformatic pipeline based on STAR, SAMTOOLS, and the R package DESeq2
Assembly: GRCh38
Supplementary files format and content: normalized_MV411_counts.csv: csv file includes normalized counts for each MV4-11 Sample
Supplementary files format and content: normalized_HEL_counts.csv: csv file includes normalized counts for each HEL Sample

source_name: HEL

growth_protocol: MV4-11 and HEL human acute myeloid leukemia cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from MV4-11 and HEL cells using the RNeasy Mini Kit (QIAGEN, 74104) per the manufacturer's instructions
Total RNA was shipped to GENEWIZ (Azenta Life Sciences) for Standard RNA-Seq service, where polyA+ transcripts were isolated and RNA-seq library was prepared per their in-house protocols

treatment_protocol:
Prior to experiment, MV4-11 and HEL cells were engineered to stably express SpCas9 protein
Additionally, prior to experiment, SpCas9-expressing MV4-11 cells were lentivirally-infected with the LRG2.1 vector containing an sgRNA targeted against ROSA26(Control) or TP53, and cells were sorted for GFP positivity
On Day 0 of experiment, cells were lentivirally-infected with the LRCherry2.1 vector containing an sgRNA targeted against ROSA26(Control) or DCAF15
On Day 3 of experiment, cells were sorted for mCherry and GFP double positivity
On Day 4 of experiment, cells were harvested and frozen for RNA extraction

value: HEL

value: acute myeloid leukemia


title: E_4_APLNrKO_ML233_3h_4


title: D_4_APLNrKO_DMSO_4


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, 11mo @RT, rep1

description:
HIC17027.hic
HIC17027_30.hic

value: Freeze-dried liver, 11mo @RT, rep1


title: HEL cells, LRCherry2.1-sgDCAF15#2, rep1


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, run over by a car

description:
HIC17023.hic
HIC17023_30.hic

value: Freeze-dried liver, run over by a car


title: AMSC_POP#9

value: subcutaneous abdominal lipoaspirate

value: primary adipose derived stromal/stem cells (AMSC or ASC)

value: serum free expansion medium supplemented with human Platelet Lysate (hPL)

value: 9-14 days

value: confluency


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, 7mo @RT, rep1

description:
HIC16916.hic
HIC16916_30.hic

value: liver

value: Freeze-dried liver, 7mo @RT, rep1


title: HEL cells, LRCherry2.1-sgROSA26(Control), rep3

value: WT


title: HEL cells, LRCherry2.1-sgROSA26(Control), rep2


title: D_3_APLNrKO_DMSO_3

value: embryo

value: KO

value: 3 dpf embryo


title: HEL cells, LRCherry2.1-sgDCAF15#2, rep3


title: AMSC_POP#8

value: pelvic organ prolapse (POP)


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +120h @RT, rep2

description:
HIC17163.hic
HIC17163_30.hic

value: Bovine liver, +120h @RT, rep2


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +120h @RT, rep1

description:
HIC17162.hic
HIC17162_30.hic

value: Bovine liver, +120h @RT, rep1


title: AMSC_POP#7


title: HEL cells, LRCherry2.1-sgROSA26(Control), rep1

value: HEL

value: acute myeloid leukemia


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +96h @RT, rep2

description:
HIC17161.hic
HIC17161_30.hic

value: Bovine liver, +96h @RT, rep2


title: D_1_APLNrKO_DMSO_1


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +84h @RT, rep2

description:
HIC17159.hic
HIC17159_30.hic

value: Bovine liver, +84h @RT, rep2


title: D_2_APLNrKO_DMSO_2


title: AMSC_Ctrl#4

value: subcutaneous abdominal lipoaspirate

value: primary adipose derived stromal/stem cells (AMSC or ASC)

value: controls - without pelvic organ prolapse (CTRL)


title: MV4-11 cells, LRG2.1-sgTP53#6, LRCherry2.1-sgDCAF15#2, rep2

value: TP53-KO + DCAF15-KO


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +72h @RT, rep2

description:
HIC17158.hic
HIC17158_30.hic

value: liver

value: Bovine liver, +72h @RT, rep2


title: C_1_WT_ML233_24h_1

value: WT


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +48h @RT, rep2

description:
HIC17156.hic
HIC17156_30.hic

value: Bovine liver, +48h @RT, rep2


title: MV4-11 cells, LRG2.1-sgTP53#6, LRCherry2.1-sgROSA26(Control), rep3


title: MV4-11 cells, LRG2.1-sgTP53#6, LRCherry2.1-sgROSA26(Control), rep2


title: AMSC_Ctrl#6

value: serum free expansion medium supplemented with human Platelet Lysate (hPL)

value: 9-14 days

value: confluency


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +96h @RT, rep1

description:
HIC17160.hic
HIC17160_30.hic

value: Bovine liver, +96h @RT, rep1


title: AMSC_Ctrl#5


title: C_3_WT_ML233_24h_3

value: embryo

value: 3 dpf embryo


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +36h @RT, rep2

description:
HIC17155.hic
HIC17155_30.hic

value: Bovine liver, +36h @RT, rep2


title: MV4-11 cells, LRG2.1-sgTP53#6, LRCherry2.1-sgDCAF15#2, rep3

value: acute myeloid leukemia


title: AMSC_Ctrl#3


title: MV4-11 cells, LRG2.1-sgTP53#6, LRCherry2.1-sgDCAF15#2, rep1


title: C_2_WT_ML233_24h_2


title: 10x_WT_Skin_CD45pos

city: Vienna

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
Demultiplxing, alignment, feature counting and filtering was performed with the 10x Genomics Cell Ranger pipeline version 5.0.1 against reference transcriptome mm10-2020-A.
Assembly: GRCm38 (UCSC mm10)
Supplementary files format and content: FASTQ files
Supplementary files format and content: 10x Genomics Cell Ranger fitered matrix HDF5

organism: Mus musculus

source_name: skin

extract_protocol: 10x Genomic Single Cell 3' v3

value: skin

value: skin cell suspension

value: female


title: AMSC_Ctrl#2

value: subcutaneous abdominal lipoaspirate

value: primary adipose derived stromal/stem cells (AMSC or ASC)

value: controls - without pelvic organ prolapse (CTRL)


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +60h @RT, rep2

description:
HIC17157.hic
HIC17157_30.hic

value: liver

value: Bovine liver, +60h @RT, rep2


title: MV4-11 cells, LRG2.1-sgROSA26(Control), LRCherry2.1-sgDCAF15#2, rep3


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +12h @RT, rep2

description:
HIC17153.hic
HIC17153_30.hic

value: Bovine liver, +12h @RT, rep2


title: MV4-11 cells, LRG2.1-sgROSA26(Control), LRCherry2.1-sgDCAF15#2, rep2


title: B_3_WT_ML233_3h_3

value: WT


title: AMSC_Ctrl#1

value: serum free expansion medium supplemented with human Platelet Lysate (hPL)

value: 9-14 days


title: C_4_WT_ML233_24h_4


title: MV4-11 cells, LRG2.1-sgTP53#6, LRCherry2.1-sgROSA26(Control), rep1


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +24h @RT, rep2

description:
HIC17154.hic
HIC17154_30.hic

value: Bovine liver, +24h @RT, rep2


title: A_4_WT_DMSO_4

value: embryo


title: MTV-high patient #7_normal

city: Seoul

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

country: South Korea

institute: Yonsei University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Pancreas cancer

extract_protocol:
Total RNAs were extracted from the tissue samples using TRizolTM Reagent (Invitrogen, MA), followed by rRNA removal using Lexogen RIBO COP rRNA deletion kit (Lexogen, Vienna, Austria).
The RNAs above 1.8 for OD260/280, 1.6 for OD260/230, and 7.0 for RNA integrity number (RIN) were used to construct RNA libraries using SMARTer® Stranded RNA-Seq Kit (Clontech Laboratories, Inc. CA).

tag: patient diagnosis

value: Pancreas cancer

value: normal pancreas

tag: metabolic tumor volume (mtv) status

value: MTV-high


title: B_2_WT_ML233_3h_2

value: 3 dpf embryo


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +84h @RT, rep1

description:
HIC17151.hic
HIC17151_30.hic

value: Bovine liver, +84h @RT, rep1


title: MV4-11 cells, LRG2.1-sgROSA26(Control), LRCherry2.1-sgROSA26(Control), rep3

value: acute myeloid leukemia


title: A_3_WT_DMSO_3


title: A_2_WT_DMSO_2


title: MV4-11 cells, LRG2.1-sgROSA26(Control), LRCherry2.1-sgROSA26(Control), rep2


title: B_1_WT_ML233_3h_1


title: MV4-11 cells, LRG2.1-sgROSA26(Control), LRCherry2.1-sgROSA26(Control), rep1


title: 10x_KO_Skin_CD45pos

value: skin

value: skin cell suspension

value: Tsc2fl/fl CD11c-cre

value: female


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +60h @RT, rep1

description:
HIC17149.hic
HIC17149_30.hic

value: liver

value: Bovine liver, +60h @RT, rep1


title: persister_D4-2, replicate 2, scRNA-seq

city: New York

first: Itai

last: Yanai

state: NY

address: 435 East. 30th St.

institute: NYU Langone Health

description: expression counts for all samples from dose response experiment including untreated vehicles (V1, V2) and treated tumors (D1.1, D1.2, D2.1, D2.2, D3.1, D3.2, D4.1, D4.2). Sample ids are attached to cell barcode names (column names).

library_source: transcriptomic single cell

data_processing:
Raw reads were processed with the CellRanger v3.1.0 (10X genomics) pipeline using cellranger count command with default parameters and with the combined human hg38/GRCh38 and mouse mm10/GRCm39 genomes and Ensembl 93 and Ensembl 104 transcriptome references, respectively, which indicates the multi-species mode of cellranger to assign the human cells based on alignment quality. Cell barcodes assigned to the human genome were used for further analyses.
Assembly: hg38/GRCh38
Supplementary files format and content: pdx_persistence_counts_all.csv.gz , expression matrix for the PDX Parpi persistence experiment. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes and more than 1000 umis expressed. Includes unfiltered protein coding genes.
Supplementary files format and content: pdx_resistance_counts_all.csv.gz, expression matrix for the PDX Parpi resistance experiment. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes and more than 500 umis expressed. Includes unfiltered protein coding genes.

source_name: high grade serous ovarian cancer, patient derived xenograft

growth_protocol: Immunodeficient six-week-old female NOD SCID gamma (NSG) (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice were purchased from Jackson Laboratory and allowed to acclimate to housing conditions. To generate HGSOC (High-Grade Serous Ovarian Cancer) PDX models of PARPi treatments, we used a previously characterized BRCA2 mutated tumor derived from PDX models (Cybulska et al. Am J. Pathol. 2018) (ID: 66799). Approximately 1×10^6 cells in a 1:1 ratio with Matrigel® Matrix (Corning, USA) were subcutaneously injected with a 27-gauge needle (BD Micro-Fine, USA) into the right lower mammary fat pad on the abdominal dorsal surface.

extract_protocol:
Tumors were minced with a razor blade and enzymatically dissociated in two steps. First, minced samples were incubated with 5 mL of digestion mix 1 (9 mL Advanced DMEM/F12, 1 mL Gentle Collagenase and 100 μL DNase I) at 37°C for 30 min, centrifuged at 1000 RPM for 4 min. After removing the supernatant, samples were incubated with 5 mL of digestion mix 2 (3 mL Advanced DMEM/F12, 2 mL Dispase, 5 mL TrypLE, 100 μL DNase I) at 37°C for 15 min, placed on a 70 μm cell strainer and washed with Advanced DMEM/F12 + 10% FBS. Samples were centrifuged at 1000 RPM for 4 min, incubated with 1 ml of ACK Lysing Buffer (ThermoFisher) for 4 min, washed with PBS + 10% FBS, resuspended in PBS, placed on a 35 μm cell strainer and viability was determined by Trypan Blue staining. Dissociated cells were collected for scRNA-Seq immediately (resistance experiment) or cryopreserved (dose-response experiment) by resuspending in freezing media (50% FBS, 40% Advanced DMEM/F12 and 10% DMSO) and stored at -80°C. Batches of replicates were processed on the same day. Frozen samples were thawed, washed in media, resuspended in PBS and the cell concentration adjusted for the 10X Genomics single-cell encapsulation protocol following library preparation and sequencing.
Library preparation was performed using the 10X Genomics Chromium platform with the Chromium Single Cell Library & Gel Bead Kit v3.1 following the manufacturer’s instructions.

treatment_protocol: To establish a drug-resistance model, tumors were treated along three passages. In a first passage, when the PDX tumors reached 100–200 mm3 tumor volume, Vehicle (10% dimethylacetamide, 5% Solutol HS15, 85% PBS) or talazoparib (0.0066mg per mouse = 0.33mg/kg, oral gavage) was administered for 5 consecutive days a week. Talazoparib treatment caused tumor remission and treatment was interrupted. Tumor sizes were followed until reappearance and treatment was reintroduced. Vehicles (V1 and V2) and drug treated tumors (R1.1 and R1.2) that did not show further regression upon re-treatment — thus indicating resistance — were collected for scRNA-Seq at the humane endpoint (1500-2000 mm3 or up to 20 mm in one dimension). A replicate tumor was implanted in a second passage and maintained under treatment upon tumor detection. The resulting tumor was implanted in a third passage, generating 3 replicates (2 talazoparib treated (R3.1 and R3.2) and 1 vehicle (R3.V)). In a second set of experiments aimed to study the persisters phenotype treated with different doses of talazoparib, mice were treated as described above with the following doses: a) Vehicle; b) Dose 1 (D1) was 0.13 mg/kg of talazoparib (Selleckchem, S7048) (n=2); c) Dose 2 (D2) was 0.23 mg/kg (n=2); d) Dose 3 (D3) was 0.33 mg/kg (n=2) and e) Dose 4 (D4) was 0.66 mg/kg. Vehicle tumors were collected at the humane endpoint and talazoparib treated tumors were collected after 50-57 days of treatment.

value: PDX nod-scid gamma (NSG) mice

value: epithelial

value: BRCA2 mutant

value: treated, talazoparib 0.66mg/kg


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +48h @RT, rep1

description:
HIC17148.hic
HIC17148_30.hic

value: Bovine liver, +48h @RT, rep1


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +36h @RT, rep1

description:
HIC17147.hic
HIC17147_30.hic

value: Bovine liver, +36h @RT, rep1


title: B_4_WT_ML233_3h_4

value: embryo

value: WT


title: MV4-11 cells, LRG2.1-sgROSA26(Control), LRCherry2.1-sgDCAF15#2, rep1


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, after 22h in dehydrator +7 days @RT

description:
HIC17152.hic
HIC17152_30.hic


title: DRIP_seq_Rnase_treated_ve_ctrl

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
FASTQ files were trimmed using trim_galore utility. During this step, adapters and low quality bases were filtered out. The fastqc utility was applied to examine data quality.
Trimmed FASTQ files were mapped to the genome, assembly hg38, with hisat2 utility.
Coverage bigwig files were created with deepTools utility bamCompare  using ration operation relative to input.
Downstream analysis was performed with R custom scripts.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: DRIP-seq

growth_protocol: MCF7 (HTB-22) were grown in RPMI supplemented with 10% (vol/vol) FBS (GIBCO), glutamine, and penicillin/streptomycin (Beit-Haemek). HMLE cells were grown in Promocell mammary epithelial cell basal media (C-21010) with added supplements (c-93110) whereas MCF10A were grown on DMEM/F12 supplemented with 5% Horse serum, 20 ng/ml EGF, 0.5 mg/ml Hydrocortisone, 100 ng/ml Cholera toxin, 10 mg/ml Insulin and Pen/Strep. MCF-7 cells were synchronized in the G1 cell cycle stage by culturing in serum-free media for 72 hours followed by replacing the media with 10% FBS media for 5 hours. Cells were grown at 37°C under a humidified atmosphere with 5% CO2. Cells were routinely authenticated by STR profiling, tested for mycoplasma, and cell aliquots from early passages were used.

extract_protocol:
cells were crosslinked with 1% formaldehyde  and quenched with glycine. Fixed cells were washed in lysis buffer. Cells were sonicated using bioruptor sonicator to produce chromatin fragments of ~200-300 bp. The chromatin was immunoprecipitated by incubation with 5 μl of anti-TOP1cc antibody (MABE1048). Immune complexes were captured with protein G Dynabeads. DNA was precipitated by phenol/chloroform/isoamylalcohol extraction. DRIP-seq was done according to the published protocol (Sanz and Chédin, 2019).
library was prepaired using kappa hyperprep kit

treatment_protocol: The knockdown in TOP1cc ChIP-seq and DRIP-seq experiments were done using the doxycycline inducible shTOP1 plasmid that was kindly obtained from Yilun Liu. For RNase H1 overexpression, RNase H1 plasmid and its empty control plasmid containing only GFP, a kind gift from Dr. Sara Selig (Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel), were used. GFP expression was used as an indicative of RNase H1 overexpression. The plasmid was prepared as described in (Sagie et al., 2017).

value: luminal breast cancer


title: DRIP_seq_shTOP1_pDOX_Rnase_H_OE

tag: treatment with dox

value: WITH DOX


title: MTV-high patient #6_cancer

value: Pancreas cancer

tag: tissue

value: pancreatic cancer

value: MTV-high


title: persister_D3-2, replicate 2, scRNA-seq

value: high grade serous ovarian cancer, patient derived xenograft

tag: cell line

value: treated, talazoparib 0.33mg/kg


title: MTV-high patient #4_cancer


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +12h @RT, rep1

description:
HIC17145.hic
HIC17145_30.hic

value: liver

value: Bovine liver, +12h @RT, rep1


title: MTV-high patient #4_normal

value: normal pancreas


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +72h @RT, rep1

description:
HIC17150.hic
HIC17150_30.hic

value: Bovine liver, +72h @RT, rep1


title: MTV-high patient #6_normal


title: MTV-high patient #3_cancer


title: A_1_WT_DMSO_1

value: 3 dpf embryo


title: persister_D4-1, replicate 1, scRNA-seq

value: PDX nod-scid gamma (NSG) mice

tag: cell type

value: epithelial

value: BRCA2 mutant

value: treated, talazoparib 0.66mg/kg


title: MTV-high patient #5_cancer


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, +24h @RT, rep1

description:
HIC17146.hic
HIC17146_30.hic

value: Bovine liver, +24h @RT, rep1


title: MTV-high patient #5_normal


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, after 22h in dehydrator

description:
HIC17143.hic
HIC17143_30.hic

value: Bovine liver, after 22h in dehydrator


title: MTV-high patient #7_cancer


title: persister_D2-1, replicate 1, scRNA-seq

tag: genotype

value: treated, talazoparib 0.23mg/kg


title: DRIP_seq_shTOP1_pDOX_EV

value: luminal breast cancer

tag: treatment

value: WITH DOX


title: Hi-C of Bos taurus DNA Zoo Sample6913, Fresh bovine liver, 2hpm, rep2

description:
HIC17141.hic
HIC17141_30.hic

value: Fresh bovine liver, 2hpm, rep2


title: MTV-high patient #2_cancer

value: Pancreas cancer

value: pancreatic cancer

value: MTV-high


title: persister_D3-1, replicate 1, scRNA-seq

value: high grade serous ovarian cancer, patient derived xenograft

value: treated, talazoparib 0.33mg/kg


title: DRIP_seq_shTOP1_mDOX_Rnase_H_OE

value: NO DOX


title: Hi-C of Bos taurus DNA Zoo Sample6913, Fresh bovine liver, 2hpm, rep3

description:
HIC17144.hic
HIC17144_30.hic

value: liver

value: Fresh bovine liver, 2hpm, rep3


title: DRIP_seq_shTOP1_mDOX_EV


title: MTV-high patient #3_normal

value: normal pancreas


title: persister_D2-2, replicate 2, scRNA-seq

value: PDX nod-scid gamma (NSG) mice

value: epithelial

value: BRCA2 mutant


title: DRIP_seq_input

value: control


title: vehicle_V1_per, replicate 1, scRNA-seq

value: untreated, vehicle


title: MTV-low patient #7_cancer

value: MTV-low


title: Hi-C of Bos taurus DNA Zoo Sample6913, Fresh bovine liver, 2hpm, rep1

description:
HIC17139.hic
HIC17139_30.hic

value: Fresh bovine liver, 2hpm, rep1


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +336h @RT

description:
HIC17058.hic
HIC17058_30.hic

source_name: muscle

value: muscle

value: Beef cheek, +336h @RT


title: TOP1cc_ChIP_seq_shTOP1_pDOX_Rnase_H_OE

data_processing:
FASTQ files were trimmed using trim_galore utility. During this step, adapters and low quality bases were filtered out. The fastqc utility was applied to examine data quality.
Trimmed FASTQ files were mapped to the genome, assembly hg38, with hisat2 utility.
Coverage bigwig files were created with deepTools utility bamCompare  using ration operation relative to input.
Downstream analysis was performed with R custom scripts.
Assembly: hg38
Supplementary files format and content: bigWig

value: luminal breast cancer

value: WITH DOX

tag: chip antibody

value: anti-TOP1cc antibody (MABE1048)


title: persister_D1-2, replicate 2, scRNA-seq

value: high grade serous ovarian cancer, patient derived xenograft

value: treated, talazoparib 0.13mg/kg


title: MTV-high patient #2_normal

value: Pancreas cancer

value: MTV-high


title: TOP1cc_ChIP_seq_input


title: vehicle_V2_per, replicate 2, scRNA-seq


title: persister_D1-1, replicate 1, scRNA-seq


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +312h @RT

description:
HIC17056.hic
HIC17056_30.hic

value: Beef cheek, +312h @RT


title: MTV-low patient #7_normal

value: normal pancreas


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +300h @RT

description:
HIC17055.hic
HIC17055_30.hic

value: Beef cheek, +300h @RT


title: TOP1cc_ChIP_seq_shTOP1_pDOX_EV


title: TOP1cc_ChIP_seq_shTOP1_mDOX_Rnase_H_OE

value: NO DOX


title: MTV-high patient #1_cancer

value: pancreatic cancer


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +288h @RT

description:
HIC17054.hic
HIC17054_30.hic

value: Beef cheek, +288h @RT


title: cov362_pool_CGATCACC,scRNA-Seq

description: expression counts tsv for all cov362 samples untreated (C) and resistant cells (T5, T10, T20, T40) where sample names are attached to cell barcodes (columns). barcodes_cov362.tsv contains cell ids, antibody_cov362.csv contains HTO sequences used for sample demultiplexing.

data_processing:
Raw reads were processed with the CellRanger v3.1 (10X genomics) pipeline using cellranger count command with default parameters and with the hg38/GRCh38 genome and Ensembl 93 transcriptome references.
Sample demultiplexing was performed using the CITE-seq-Count pipeline (v1.4.3, https://github.com/Hoohm/CITE-seq-Count). Example: CITE-Seq-Count -R1 BS04614A_S9_L001_R1_001.fastq.gz -R2 BS04614A_S9_L001_R2_001.fastq.gz -cbf 1 -cbl 16 -umif 17 -umil 28 --max-error 1 --dense -T 10 -wl barcodes_ovsaho.tsv -t antibody_ovsaho.csv -o output. The following HTOs correspond to the following samples: Ovsaho: HTO1: C, HTO2: T5, HTO3: T10, HTO4: T20, HTO5: T40. COV362: HTO6: C, HTO7: T5, HTO8: T10, HTO9: T20, HTO10: T40. Seurat was used to assign cells to HTOs according to https://satijalab.org/seurat/articles/hashing_vignette
Assembly: hg38/GRCh38
Supplementary files format and content: ovsaho_count_matrix.tsv, cov362_count_matrix.tsv, expression matrix of cells from ovsaho and cov362 pooled libraries containing cells from the following conditions: C, T5, T10, T20, T40. Sample ids are attached to the cell barcodes (column names). Cells were filtered based on expression of less than 15% of mitochondrial genes, more than 500 genes and more than 700 umis expressed and less than average plus two standard deviations of umi counts. Includes unfiltered protein coding genes.
Supplementary files format and content: antibody_ovsaho.csv, antibody_cov362.csv, hto antibodies and sequence correspondence for demultiplexing
Supplementary files format and content: barcodes_ovsaho.csv, barcodes_cov362.csv, cell ids used for demultiplexing

source_name: Cell line

growth_protocol: Ovsaho cells were cultured in RPMI-1640 (ThermoFisher) with 10% Fetal Bovine Serum (FBS), 1% L-Glutamine 200 mM, 1% Penicillin and Streptomycin (10,000 U/mL, ThermoFisher). COV362 cells were cultured in DMEM (ThermoFisher) supplemented with 10% FBS, 1% L-Glutamine and 1% Penicillin and Streptomycin.

extract_protocol:
Cells were trypsinized and single-cell suspensions were counted and pooled for cell hashing method using Total-SeqA hashtag oligos HTO 1-10 (Biologend) according to manufacturers protocol. The cell pool was loaded for droplet-based scRNA-Seq using the 10X Genomics Chromium platform according to the manufacturer's protocol.
Library preparation was performed using the 10X Genomics Chromium platform with the Chromium Single Cell 30 Library & Gel Bead Kit v3.1 following the manufacturer’s instructions. For the hashtag oligos, 1μl of HTO PCR additive primer was added to the 10X cDNA amplification step, and the supernatant from the 0.6X cDNA cleanup was kept and processed according to the Cell Hashing protocol, with 14 PCR cycles and a 1.2X cleanup after the PCR. Libraries were diluted to 2 nM and 75bp paired-end sequencing was performed using the Illumina NextSeq 500

treatment_protocol: Ovsaho and Cov362 cells were treated in dose escalation experiments from 1 uM to 40 uM of olaparib to generate drug resistant populations. The populations resistant to 5 uM (T5), 10 uM (T10), 20 uM (T20) and 40 uM (T40) and unexposed (C) cells were collected for single-cell RNA-Seq using the 10X Genomics platform.

value: Cell line

value: Epithelial

value: untreated and treated cells with 10uM or 320uM of olaparib


title: MTV-low patient #6_normal

value: MTV-low


title: MTV-high patient #1_normal


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +276h @RT

description:
HIC17053.hic
HIC17053_30.hic

value: muscle

value: Beef cheek, +276h @RT


title: cov362_hashing_TCCGGAGA ,hto


title: TOP1cc_ChIP_seq_shTOP1_mDOX_EV

value: luminal breast cancer

value: anti-TOP1cc antibody (MABE1048)


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +324h @RT

description:
HIC17057.hic
HIC17057_30.hic

value: Beef cheek, +324h @RT


title: CEL_seq_TOP1_KD_Rnase_H_OE_rep4

data_processing:
FASTQ files were trimmed using trim_galore utility. During this step, adapters, polyA tails and low quality bases were filtered out. The fastqc utility was applied to examine data quality.
Trimmed FASTQ files were mapped to the genome, assembly hg38, with hisat2. Resulting BAM files were then UMI de-duplicated using umi_tools, dedup function.
De-duplicated BAM files were input to R Rsubread::featureCounts function to create a gene count table with minOverlap=20, fracOverlap=0.99 and no countMultiMappingReads.
Downstream analysis was performed with R custom scripts.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including raw counts per gene per sample.

growth_protocol: MCF7 (HTB-22) were grown in RPMI supplemented with 10% (vol/vol) FBS (GIBCO), glutamine, and penicillin/streptomycin (Beit-Haemek). . Cells were grown at 37°C under a humidified atmosphere with 5% CO2. Cells were routinely authenticated by STR profiling, tested for mycoplasma, and cell aliquots from early passages were used.

extract_protocol:
Total RNA was extracted using TRI reagent (BioLabs) according to the manufacturer specifications. RNA concentration was measured using Qubit Flex Fluorometer (ThermoFisher Scientific). RNA sequencing libraries were prepared using the CEL-Seq2 protocol in the Technion genomic Center (TGC), as published by (Hashimshony et al., 2012), with one modification; instead of single-cells as input, 2 ng purified RNA was taken as input for library preparation. The CEL-Seq2 libraries were analyzed for average fragment size using Agilent 2200 TapeStation (Agilent) and concentration was measured using Qubit Flex Fluorometer (ThermoFisher Scientific). The libraries were sequenced on the Illumina NextSeq 2000 sequencer (Illumina), 12 bases for read 1 and 88 bases for read 2. Demultiplexing was performed in two steps
as published by (Hashimshony et al., 2012)
CEL-seq

treatment_protocol: Transient transfection of siTOP1 (Dharmacon; SMARTpool siRNA, L-005278-00-0005) and siSc (Dharmacon; D-00181010) was achieved using lipofectamine (ThermoFisher). Cells were seeded to reach a confluency of 60-70% on the day of transfection. Transfection solution was prepared by mixing 1.5ml serum/antibiotic-free RPMI with 30μL lipofectamine and incubating for 5 minutes, before adding a mixture of 1.5ml RPMI and 0.6nmoles of siRNA followed by 20 minutes incubation at RT. The mixture was then added to the cells in a 10cm plate cultured in antibiotic/serum-free media. The media was replaced by fully supplemented media after 5-6 hours, and cells were incubated in the incubator for 48 hours. For RNase H1 overexpression, RNase H1 plasmid and its empty control plasmid containing only GFP, a kind gift from Dr. Sara Selig (Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel), were used. GFP expression was used as an indicative of RNase H1 overexpression. The plasmid was prepared as described in (Sagie et al., 2017).

value: TOP1 siRNA + RNase H OE


title: MTV-low patient #6_cancer

value: Pancreas cancer


title: cov362_pool_GATCTTGA,scRNA-Seq


title: CEL_seq_TOP1_KD_Rnase_H_OE_rep3


title: CEL_seq_TOP1_KD_Rnase_H_OE_rep2


title: MTV-low patient #5_normal


title: cov362_pool_ACGGACAT,scRNA-Seq


title: MTV-low patient #5_cancer


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +240h @RT

description:
HIC17050.hic
HIC17050_30.hic

value: Beef cheek, +240h @RT


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +264h @RT

description:
HIC17052.hic
HIC17052_30.hic

value: Beef cheek, +264h @RT


title: ovsaho_pool_GAATTCCA,scRNA-Seq

description: expression counts tsv for all ovsaho samples untreated (C) and resistant cells (T5, T10, T20, T40) where sample names are attached to cell barcodes (columns). barcodes_ovsaho.tsv contains cell ids, antibody_ovsaho.csv contains HTO sequences used for sample demultiplexing.

value: Ovsaho

value: untreated and treated cells with 5, 10, 20 and 40 uM of olaparib


title: CEL_seq_TOP1_KD_EV_rep3

value: TOP1 siRNA+EV


title: cov362_pool_TTCAGGTG,scRNA-Seq


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +252h @RT

description:
HIC17051.hic
HIC17051_30.hic

value: Beef cheek, +252h @RT


title: MTV-low patient #4_normal

value: normal pancreas


title: MTV-low patient #4_cancer

value: pancreatic cancer


title: CEL_seq_TOP1_KD_EV_rep4


title: MTV-low patient #3_cancer


title: ovsaho_hashing_ATTACTCG,hto

value: Cell line

value: Epithelial


title: CEL_seq_TOP1_KD_EV_rep2


title: ovsaho_pool_ACGCGGGT,scRNA-Seq


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +216h @RT

description:
HIC17048.hic
HIC17048_30.hic

value: muscle

value: Beef cheek, +216h @RT


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +228h @RT

description:
HIC17049.hic
HIC17049_30.hic

value: Beef cheek, +228h @RT


title: CEL_seq_TOP1_KD_EV_rep1

value: luminal breast cancer


title: MTV-low patient #3_normal

value: MTV-low


title: ovsaho_pool_TTTACATG,scRNA-Seq


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +204h @RT

description:
HIC17047.hic
HIC17047_30.hic

value: Beef cheek, +204h @RT


title: CEL_seq_ctrl_siRNA_Rnase_H_OE_rep4

value: ctrl siRNA+RNase H OE


title: MTV-low patient #2_cancer

value: Pancreas cancer


title: CEL_seq_TOP1_KD_Rnase_H_OE_rep1

value: TOP1 siRNA + RNase H OE


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +192h @RT

description:
HIC17046.hic
HIC17046_30.hic

value: Beef cheek, +192h @RT


title: kura_pool_rep2_hashing_ATTCAGAA,replicate 2,CITE-Seq HTO

description: expression counts for all samples where sample names are attached to cell barcodes (columns). barcodes.tsv contains cell ids and antibody_ref.csv contains HTO sequences used for demultiplexing.

data_processing:
Raw reads were processed with the CellRanger v3.1 (10X genomics) pipeline using cellranger count command with default parameters and with the hg38/GRCh38 genome and Ensembl 93 transcriptome references.
Sample demultiplexing was performed using the CITE-seq-Count pipeline (v1.4.3, https://github.com/Hoohm/CITE-seq-Count). Example: CITE-Seq-Count -R1 BS04600A_S9_L001_R1_001.fastq.gz -R2 BS04600A_S9_L001_R2_001.fastq.gz -cbf 1 -cbl 16 -umif 17 -umil 28 --max-error 1 --dense -T 10 -wl barcodes_R1.tsv -t antibody_ref.csv -o output. The following HTOs correspond to the following samples: Replicate1: HTO1: C.R1, HTO2: T10.A.R1, HTO3: T10.P.R1, HTO4: T320.A.R1, HTO5: T320.P.R1. Replicate2: HTO6: C.R2, HTO7: T10.A.R2, HTO8: T10.P.R2, HTO9: T320.A.R2, HTO10: T320.P.R2 Seurat was used to assign cells to HTOs according to https://satijalab.org/seurat/articles/hashing_vignette
Assembly: hg38/GRCh38
Supplementary files format and content: kuramochi_counts_all_C_P10_P320_T10_T320.csv.gz, expression matrix of cells from replicates 1 (R1) and 2 (R2) for pooled libraries containing cells from the following conditions: C, T10.P, T10.A, T320.P, T320.A for both replicates (R1, R2). Sample ids are attached to the cell barcodes (column names). Cells were filtered based on expression of less than 15% of mitochondrial genes, more than 500 genes and more than 700 umis expressed and less than average plus two standard deviations of umi counts. Includes unfiltered protein coding genes.
Supplementary files format and content: antibody_ref.csv, contains HTO antibodies and correspondent sequences used for sample demultiplexing the pooled scRNA-seq libraries based on the CITE-Seq method.
Supplementary files format and content: barcodes_R1.csv, barcodes_R2.csv, cell ids used for demultiplexing together with antibody_ref.csv using the CITE-Seq count pipeline.

growth_protocol: Cells were cultured in RPMI-1640 (ThermoFisher) with 10% Fetal Bovine Serum (FBS), 1% MEM Non-Essential Amino Acids, 1% L-Glutamine 200 mM, 1% Antibiotic-Antimycotic solution 100X and 0.25 U/mL insulin solution (Sigma-Aldrich)

treatment_protocol: Kuramochi cells were exposed to 10 uM (P10 and T10) and 320 uM (P320, T320) of olaparib for 9 days to generate persister populations (T10.P and T320.P) from acute drug exposure. The experiment also included adapted (olaparib resistant) populations at the same doses (T10.A and T320.A) and untreated controls (C). Cells were then collected for single-cell RNA-Seq using the 10X Genomics platform.

value: Kuramochi

value: untreated and treated cells with 10uM or 320uM of olaparib


title: CEL_seq_ctrl_siRNA_Rnase_H_OE_rep3


title: MTV-low patient #2_normal


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +180h @RT

description:
HIC17045.hic
HIC17045_30.hic

value: Beef cheek, +180h @RT


title: CEL_seq_ctrl_siRNA_Rnase_H_OE_rep2


title: kura_pool_rep2_AGGCGTCA,replicate 2,scRNA-Seq


title: MTV-low patient #1_cancer


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +168h @RT

description:
HIC17044.hic
HIC17044_30.hic

value: Beef cheek, +168h @RT


title: kura_pool_rep2_TCTATATC,replicate 2,scRNA-Seq


title: CEL_seq_ctrl_siRNA_Rnase_H_OE_rep1


title: ovsaho_pool_CGCGATAC,scRNA-Seq

value: Ovsaho

value: untreated and treated cells with 5, 10, 20 and 40 uM of olaparib


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +156h @RT

description:
HIC17043.hic
HIC17043_30.hic

value: Beef cheek, +156h @RT


title: MTV-low patient #1_normal

value: normal pancreas


title: kura_pool_rep2_CTAGCGAG,replicate 2,scRNA-Seq

value: Cell line

value: Epithelial


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +144h @RT

description:
HIC17042.hic
HIC17042_30.hic

value: muscle

value: Beef cheek, +144h @RT


title: kura_pool_rep2_GACTACGT,replicate 2,scRNA-Seq


title: kura_pool_rep1_hashing_GAGATTCC,replicate 1,CITE-Seq HTO


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +132h @RT

description:
HIC17041.hic
HIC17041_30.hic

value: Beef cheek, +132h @RT


title: CEL_seq_ctrl_siRNA_EV_rep3

value: luminal breast cancer

value: ctrl siRNA + EV


title: shRNAseq in W22 roots Rep2

city: Cold Spring Harbor

first: Jonathan

last: Cahn

address: 1 Bungtown Rd

institute: CSHL

data_processing:
Adapter trimming with cutadapt
For RNAseq and RAMPAGE: mapping to W22 v2 genome with STAR (parameters: --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 20 --quantMode GeneCounts).
For RAMPAGE only, TSS were identified by calling peak with macs2 using the corresponding RNAseq control.
For shRNA, trimmed fastq files were depleted of snoRNAs, rRNAs and tRNAs by mapping to these structural RNAs from zea mays with bowtie2, and the leftover reads were mapped to W22 v2 with ShortStack (--mmap u --dicermin 20 --dicermax 24 --bowtie_m all --mismatches 1 --foldsize 1000 --pad 250)
Assembly: W22 v2
Supplementary files format and content: For RNAseq: count table on all W22 v2 genes for each sample (combined ReadsPerGene.out.tab files from STAR)
Supplementary files format and content: For RAMPAGeE: list of identified TSS (macs2 narrowPeak format)
Supplementary files format and content: For shRNA: table of identified clusters (ShortStack Results file)

organism: Zea mays

source_name: root tips

growth_protocol: For collecting immature ears, W22 maize inbreds were grown in the CSHL Uplands Farm field in the summer until they reached the appropriate stage. The plants were collected from the field, and 5-10mm primary and secondary ear primordia were dissected in the lab then frozen in LN2 and stored at -80°C. For pollen samples, shedding tassels of field-grown plants as described above were bagged in the evening and mature pollen was collected the following day. After passing through a sieve to remove anthers, pollen was frozen in LN2 and stored at -80°C. For endosperm samples, ears of field-grown plants were sib-pollinated and collected 15 DAP. Endosperm was dissected in the lab, frozen in LN2 and stored in -80°C. For root tips samples, seeds were germinated on wet paper towels in a Pyrex dish kept in the incubator at 26°C in continuous darkness. After 5 days, 1-3 mm root tips were cut off with a razor blade on ice, frozen in LN2 and stored at -80°C. For coleoptilar nodes samples, seeds were germinated in flats in a long day (8h dark/16h light) growth chamber, 27°C day and 24°C night, and light at 130 μmoles at the top flat. After 5 days, seedlings were unearthed and 5 mm sections around coleoptilar nodes were dissected on ice, frozen in LN2 and stored at -80°C.

extract_protocol:
RNA was extracted with Direct-zol RNA Miniprep Kit (Zymo Reserach).
RNAseq libraries were constructed from 1ug of total RNA with TruSeq Stranded Total RNA LT Kit, including RiboZero Plant depletion and oligo(dT) and random probes for cDNA synthesis. RAMPAGE libraries were constructed from 5ug total RNA following published protocol (Batut and Gingeras 2013) using RiboMinus Plant depletion. shRNAseq libraries were constructed from 5ug of total RNA using TruSeq Small RNA protocol after RiboMinus Plant depletion and size selection of 100 to 205nt with BluePippin (Sage Science).

value: root tips

tag: inbred line

value: WT

value: 5 DAG


title: CEL_seq_ctrl_siRNA_EV_rep2


title: shRNAseq in W22 pollen Rep2

source_name: pollen

value: pollen

value: mature pollen


title: kura_pool_rep1_TATCGATA,replicate 1,scRNA-Seq

value: Kuramochi

value: untreated and treated cells with 10uM or 320uM of olaparib


title: CEL_seq_ctrl_siRNA_EV_rep1


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +108h @RT

description:
HIC17039.hic
HIC17039_30.hic

value: Beef cheek, +108h @RT


title: shRNAseq in W22 pollen Rep1


title: sBLISS_MCF7_G1_synch_rep2

data_processing:
FASTQ files were trimmed using trim_galore utility. During this step, adapters (two runs) and low quality bases were filtered out. The fastqc utility was applied to examine data quality.
Trimmed FASTQ files were mapped to the genome, assembly hg38, with hisat2. Resulting BAM files were then UMI de-duplicated using umi_tools, dedup function.
De-duplicated BAM files were converted to SAM files and transformed to BLISS bedGraph files using a custom Python script.
BedGraph files were converted to bigWig files with bedGraphToBigWig utility.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file consisting of BLISS breaks counts per gene per sample.
Library strategy: BLISS-seq

extract_protocol:
sBLISS was performed as described in (Bouwman et al., 2020).
library indexing and amplification was performed using NEBNext® Ultra™ II Q5® Master Mix.
in-suspension break labelling in situ and sequencing (sBLISS)

treatment_protocol: Transient transfection of siTOP1 (Dharmacon; SMARTpool siRNA, L-005278-00-0005) and siSc (Dharmacon; D-00181010) was achieved using lipofectamine (ThermoFisher). Cells were seeded to reach a confluency of 60-70% on the day of transfection. Transfection solution was prepared by mixing 1.5ml serum/antibiotic-free RPMI with 30μL lipofectamine and incubating for 5 minutes, before adding a mixture of 1.5ml RPMI and 0.6nmoles of siRNA followed by 20 minutes incubation at RT. The mixture was then added to the cells in a 10cm plate cultured in antibiotic/serum-free media. The media was replaced by fully supplemented media after 5-6 hours, and cells were incubated in the incubator for 48 hours. For RNase H1 overexpression, RNase H1 plasmid and its empty control plasmid containing only GFP, a kind gift from Dr. Sara Selig (Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel), were used. GFP expression was used as an indicative of RNase H1 overexpression. The plasmid was prepared as described in (Sagie et al., 2017). For estradiol treated cells, MCF-7 cells were hormonally starved by growing in RPMI media supplemented with 10% charcoal stripped fetal bovine serum for 48 hours. Transcription was induced by replacing the media with RPMI media supplemented with charcoal stripped FBS and 100nM β-Estradiol (Sigma-Aldrich) (pre-dissolved in ethanol) and incubated for 1 hour.

value: cultured in serum-free media for 72 hours


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +120h @RT

description:
HIC17040.hic
HIC17040_30.hic

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

value: Beef cheek, +120h @RT


title: kura_pool_rep1_AGAGTCGC,replicate 1,scRNA-Seq

value: Cell line


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +96h @RT

description:
HIC17038.hic
HIC17038_30.hic

value: Beef cheek, +96h @RT


title: shRNAseq in W22 endosperm Rep2

source_name: endosperm

value: endosperm

value: 15 DAP


title: shRNAseq in W22 endosperm Rep1


title: kura_pool_rep1_GTGTCGCT,replicate 1,scRNA-Seq

value: Epithelial


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +84h @RT

description:
HIC17037.hic
HIC17037_30.hic

value: muscle

value: Beef cheek, +84h @RT


title: sBLISS_MCF7_G1_synch_rep1

value: luminal breast cancer


title: kura_pool_rep1_CCCAATAG,replicate 1,scRNA-Seq


title: sBLISS_MCF10A_RAS_transformed_rep2

value: normal breast epithelial

value: RAS transformed


title: CEL_seq_ctrl_siRNA_EV_rep4

value: ctrl siRNA + EV


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +72h @RT

description:
HIC17036.hic
HIC17036_30.hic

value: Beef cheek, +72h @RT


title: kuramochi_T320_drug_end

description: count matrix of sgRNAs from initial and end points of the screen, columns are sample ids

data_processing:
Sequencing reads were mapped to the sgRNA library sequences with MAGeCK-count algorithm (Li et al., Genome Biology 2014): mageck count -l Large_metabolic_library_sgRNA_sequence_human.txt --reverse-complement --n output --sample-label sample_labels --fastq fastq_files. The sgRNAs counts for each pair of conditions (initial and end) for treated versus control samples (C) were used as inputs for the MAGeCK-MLE algorithm (Li et al., Genome Biology 2015) to calculate gene scores.
Assembly: hg38/GRCh38
Supplementary files format and content: Large_metabolic_library_sgRNA_sequence_human.tsv, sgRNA sequences
Supplementary files format and content: kuramochi_C_T10_T320_sgrna_counts.tsv, sgRNA counts per sample and condition. Columns are samples and conditions.
Library strategy: CRISPR-Screen

extract_protocol:
Cells were trypsinized and single-cell suspensions were counted and pellets were frozen for genomic DNA extraction according to Birsoy et al. Cell, 2015.
An initial pool of cells was harvested for genomic DNA extraction as in Birsoy et al. 2015. Remaining cells were cultured for 10 population doublings either off (C, T10, T320) and on olaparib treatment (C in 1 μl and T320 in 40 μl), after which cells were harvested for genomic DNA extraction. sgRNA inserts were PCR-amplified, gel purified, quantified with NEBNext Library Quantification Kit (#E7630S) and sequenced on a Illumina NextSeq 500, generating between 20-40 million paired reads for each library.

treatment_protocol: The human metabolic CRISPR/Cas9 knockout library was obtained from the laboratory of Kivanc Birsoy (Birsoy et al. Cell, 2015). Virus was produced by cotransfection of human embryonic kidney–293 (HEK293) cells with lentiviral library pool with packaging vectors (psPAX2 and VSV-G) using PEI Pro (PolyPlus). The titer of lentiviral supernatants was determined by infecting target cells with several amounts of virus in the presence of polybrene (8 μg/ml; Millipore), counting the number of puromycin-resistant infected cells after 3 days of selection. Kuramochi C, T10 and T320 (CD44high/CD24low sorted populations) cells were infected at a multiplicity of infection of ~0.3 and selected with puromycin (4 μg/ml) 48 hours after infection. An initial pool of cells was harvested for genomic DNA extraction (initial point of the screen) as in Birsoy et al. 2015. Remaining cells were cultured for 10 population doublings either off (C, T10, T320) and on olaparib treatment (C in 1 μl and T320 in 40 μl), after which cells were harvested for genomic DNA extraction, constituting the end point of the screen.

value: Kuramochi

value: treatment with 40uM of olaparib, screen end time point


title: shRNAseq in W22 ears Rep2

source_name: immature ears

value: immature ears

value: WT


title: kuramochi_T320_end

value: untreated, screen end time point


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +60h @RT

description:
HIC17035.hic
HIC17035_30.hic

value: Beef cheek, +60h @RT


title: shRNAseq in W22 roots Rep1

value: root tips

value: 5 DAG


title: shRNAseq in W22 coleoptilar node Rep2

source_name: coleoptilar nodes

value: coleoptilar nodes


title: sBLISS_MCF10A_RAS_transformed_rep1


title: kuramochi_T320_t0

value: Cell line

value: Epithelial

value: untreated, screen initial time point


title: sBLISS_MCF10A_WT_rep1

value: NT


title: shRNAseq in W22 coleoptilar node Rep1


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +36h @RT

description:
HIC17033.hic
HIC17033_30.hic

value: muscle

value: Beef cheek, +36h @RT


title: sBliss_HMLE_rep4

source_name: HMLE

value: HMLE

value: normal mammary epithelial


title: kuramochi_T10_end

value: Kuramochi


title: RAMPAGE in W22 roots Rep2

library_source: other

molecule: other


title: kuramochi_T10_t0


title: sBliss_HMLE_rep3


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +12h @RT

description:
HIC17031.hic
HIC17031_30.hic

value: Beef cheek, +12h @RT


title: RAMPAGE in W22 roots Rep1


title: sBliss_HMLE_rep2


title: RAMPAGE in W22 pollen Rep2

value: pollen

value: mature pollen


title: sBliss_HMLE_rep1


title: kuramochi_C_nodrug_end

value: untreated, screen end time point


title: shRNAseq in W22 ears Rep1

value: immature ears

value: WT


title: sBLISS_MCF10A_WT_rep2

value: normal breast epithelial


title: RAMPAGE in W22 pollen Rep1


title: sBLISS_TOP1_KD_E2_rep2

value: luminal breast cancer

value: TOP1 siRNA + estradiol


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +48h @RT

description:
HIC17034.hic
HIC17034_30.hic

value: Beef cheek, +48h @RT


title: Macaque_PFC_Hi-C

city: Beijing

first: Ying

last: Liu

address: 5 Summer Palace Road, Haidian District, Beijing

department: College of Future Technology

country: China

institute: Peking University

description: Hi-C of PFC of adult rhesus macaque

data_processing:
Basecalling was performed using Illunima Casava (version: 1.8).
We used HiC-Pro (version: 2.11.1) to perform preprocessing for Hi-C data of PFC of human and rhesus macaque. Paired-end reads in FASTQ file format were first aligned against the reference genome (GRCh38/hg38 for human and rheMac10Plus (40 gaps filling based on Mmul_10/rheMac10)  for rhesus macaque) using Bowtie 2 (version: 2.3.5) with following parameters, global mapping: -very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder; local mapping: -very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder.
Stringent filtering processes were performed following HiC-Pro standard workflow to generate genome-wide valid contact pairs.
Cooltools (version: 0.8.8) was used to identify A/B compartments at 100 Kb resolution, with the genome divided into two distinct groups based on the sign of the first PC (PC1). The group with higher gene density was defined as compartment A, and the other was compartment B. TAD boundaries were detected using the insulation score method (Crane et al., 2015) at a resolution of 40 Kb. Consequently, TAD bodies were defined as genomic regions between two adjacent boundaries. Chromatin loops were called by HiCCUPS (version: 1.9.9) at 25 Kb resolution.
Assembly: Mmul_10 (40 gaps filling)
Supplementary files format and content: *.bed files refer to the genomic coordinates of 3D genome organizations, including A/B compartments, TADs and TAD boundaries.
Supplementary files format and content: *bedpe files refer to the genomic coordinates of chromatin loops.

organism: Macaca mulatta

source_name: Brain

extract_protocol:
0.2 g frozen PFC sample was ground in liquid nitrogen and prepared into cell suspension. The filtered cell suspensions were fixed in 1% formaldehyde for 30 min. The cross-linked DNA was digested with 200U MboI, and the digested fragment ends were filled with biotin-14-dATP, dCTP, dGTP and dTTP by DNA Polymerase I Klenow Fragment (NEB, #M0210L). The resulting blunt-end fragments were re-ligated by T4 DNA ligase. Then, the ligated cross-linked DNA was reversed by proteinase K. DNA purification was performed by removing biotin from unligated ends using T4 DNA polymerase. The resulting purified DNA was sheared to a length of 350~500 bp using Covaris M220 and biotin-labeled DNA was pulled down with Dynabeads M-280 Streptavidin (Invitrogen). The library preparation including end repair, adapter ligation and PCR amplification was performed using DNA library preparation kit (Vazyme, #ND607). The resulting libraries were sequenced by Illumina 150 bp paired-end sequencing.
Hi-C libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, #ND607) following manufacturer's instructions.

value: Wild type

tag: Sex

value: Male

tag: age

value: 26 years post birth

value: Prefrontal cortex (PFC)


title: RAMPAGE in W22 endosperm Rep1

value: endosperm

value: 15 DAP


title: kuramochi_T320W_drug,replicate 2,ATAC-Seq

description: table containing consensus peaks across samples and read counts (C, T5 to T320,P10,P320), bigwig merged of the two T320W replicates on drug

data_processing:
Raw reads were processed to remove adapter sequences using Trim Galore (-q 20, - --length 30). Filtered reads were aligned to the human genome (hg38/GRCh38) with Bowtie2 (--very-sensitive, -k 10, -X 2000). After removing reads mapping to mitochondrial DNA and duplicate reads removed with Picard Tools MarkDuplicates, only properly mapped pairs assigned by SAMTools were included for further analysis. To avoid peak detection bias due to sequencing depth differences, read depth across samples was downsampled with SAMTools to match the lowest depth.
Peak calling was performed with MACS2 and blacklisted regions were excluded. Reproducible peaks between replicates for each sample were determined using the IDR framework and peaks with high reproducibility (IDR score < 0.05) were considered.
A consensus peak set across all samples was constructed by merging the reproducible peaks from each sample using HOMER v4.1. Finally, a read count table for the consensus peaks was generated using deepTools 3.1 and differential accessibility was determined using DESeq2.
To generate bigwig files to compare the peak signal across C, the parental T320 with T320 and T320W on and off drug, the filtered bam files for both replicates were merged and the coverage was determined using deepTools 3.5.1 using bamCoverage -b processed_bam -o output.bw --outFileFormat bigwig --binSize 1 --normalizeUsing RPGC
Assembly: hg38/GRCh38
Supplementary files format and content: consensus_peaks_kuramochi_all.tsv.gz, read counts for all samples for the defined consensus peaks.
Supplementary files format and content: bigwig files (merged replicates) for C, parental T320, T320 on drug, T320 off drug, T320W on drug, T320W off drug.

extract_protocol:
Cells were trypsinized and single-cell suspensions were counted. Cell sorting based on CD24 and CD44 expression was performed on C, T5 to T320. After PBS washing, approximately 50,000 cells per sample were used for library preparation.
Library preparation was performed according to the Omni-ATAC protocol (Corces et al. Nature Methods, 2017) and paired-end libraries were sequenced on a Illumina NextSeq 500.

treatment_protocol: Kuramochi resistant cells were exposed to their respective doses of olaparib that they adapted to (5 uM to 320 uM, T5 to T320 populations) and sorted based on their CD24/CD44 profiles. Persister cells were generated by exposure to 10 uM (P10) and 320 uM (P320) of olaparib for 9 days. Untreated cells (C) were included. In addition the T320 population was cultured for 120 days without drug (T320W_nodrug), and then re-exposed to 320 uM of olaparib for 2 days (T320W_drug). The parental T320 without drug treatment (T320_nodrug) and re-exposed to drug for 2 days (T320_drug) were also generated for ATAC-Seq analyses. The resistant T5 to T320 cells were sorted based on their CD24 (low) and CD44 (high) profiles. All samples were generated in duplicates.

value: Cell line

value: Kuramochi

value: Epithelial

value: treated with 320 uM of olaparib (2 days)


title: RAMPAGE in W22 ears Rep2


title: kuramochi_T320W_nodrug,replicate 2,ATAC-Seq

description: table containing consensus peaks across samples and read counts (C, T5 to T320,P10,P320), bigwig merged of the two T320W replicates off drug

value: untreated


title: RAMPAGE in W22 endosperm Rep2


title: kuramochi_T320W_drug,replicate 1,ATAC-Seq


title: sBLISS_TOP1_KD_E2_rep1


title: sBLISS_ctrl_siRNA_vehicle_rep2

value: ctrl siRNA + EtOH


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek, +24h @RT

description:
HIC17032.hic
HIC17032_30.hic

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: muscle

value: Beef cheek, +24h @RT


title: RAMPAGE in W22 ears Rep1

value: immature ears

value: WT


title: kuramochi_T320W_nodrug,replicate 1,ATAC-Seq


title: kuramochi_T320_drug,replicate 2,ATAC-Seq

description: table containing consensus peaks across samples and read counts (C, T5 to T320,P10,P320), bigwig merged of the two T320 replicates on drug


title: kuramochi_C_drug_end

value: treatment with 1uM of olaparib, screen end time point


title: sBLISS_ctrl_siRNA_E2_rep1

value: luminal breast cancer

value: ctrl siRNA + estradiol


title: sBLISS_ctrl_siRNA_E2_rep2


title: RAMPAGE in W22 coleoptilar node Rep1

value: coleoptilar nodes

value: 5 DAG


title: sBLISS_ctrl_siRNA_vehicle_rep1


title: kuramochi_C_t0

value: untreated, screen initial time point


title: sBLISS_E2_Rnase_H_OE_rep2

value: estradiol + RNase H OE


title: kuramochi_T320_drug,replicate 1,ATAC-Seq

value: Cell line


title: RNAseq in W22 roots Rep2

value: root tips


title: Hi-C of Bos taurus DNA Zoo Sample6835, Beef cheek degradation control

description:
HIC17030.hic
HIC17030_30.hic

value: Beef cheek degradation control


title: kuramochi_T320_nodrug,replicate 2,ATAC-Seq

description: table containing consensus peaks across samples and read counts (C, T5 to T320,P10,P320), bigwig merged of the two T320 replicates off drug

value: Kuramochi

value: Epithelial


title: sBLISS_E2_Rnase_H_OE_rep1


title: RNAseq in W22 roots Rep1


title: kuramochi_T320_nodrug,replicate 1,ATAC-Seq

value: untreated


title: sBLISS_E2_EV_rep2

value: estradiol + EV


title: RNAseq in W22 pollen Rep2

value: pollen

value: mature pollen


title: kuramochi_P320,replicate 2,ATAC-Seq

description: table containing consensus peaks across samples and read counts (C, T5 to T320,P10,P320)

value: treated with 320 uM of olaparib (acute exposure 9 days)


title: sBLISS_E2_EV_rep1


title: RNAseq in W22 endosperm Rep2

value: endosperm

value: WT

value: 15 DAP


title: kuramochi_P320,replicate 1,ATAC-Seq


title: RAMPAGE in W22 coleoptilar node Rep2

value: coleoptilar nodes


title: kuramochi_P10,replicate 2,ATAC-Seq

value: treated with 10 uM of olaparib (acute exposure 9 days)


title: kuramochi_P10,replicate 1,ATAC-Seq


title: sBLISS_vehicle_EV_rep1

value: luminal breast cancer

value: ETOH+EV


title: RNAseq in W22 endosperm Rep1


title: RNAseq in W22 ears Rep2

value: immature ears


title: kuramochi_T320,replicate 2,ATAC-Seq

description: table containing consensus peaks across samples and read counts (C, T5 to T320,P10,P320), bigwig merged of the two T320 replicates

value: Cell line

value: treated with 320uM of olaparib


title: sBLISS_TOP1_KD_Rnase_H_OE_rep2

value: TOP1 siRNA + RNase H OE


title: sBLISS_vehicle_EV_rep2


title: RNAseq in W22 ears Rep1


title: sBLISS_TOP1_KD_Rnase_H_OE_rep1


title: kuramochi_T320,replicate 1,ATAC-Seq

value: Kuramochi

value: Epithelial


title: sBLISS_TOP1_KD_EV_rep2

value: TOP1 siRNA+EV


title: kuramochi_T80,replicate 2,ATAC-Seq

value: treated with 80uM of olaparib


title: kuramochi_T80,replicate 1,ATAC-Seq


title: RNAseq in W22 coleoptilar node Rep1

value: 5 DAG


title: sBLISS_TOP1_KD_EV_rep1


title: kuramochi_T160,replicate 2,ATAC-Seq

value: treated with 160uM of olaparib


title: RNAseq in W22 coleoptilar node Rep2


title: sBLISS_ctrl_siRNA_Rnase_H_OE_rep2

value: ctrl siRNA+RNase H OE


title: sBLISS_ctrl_siRNA_Rnase_H_OE_rep1


title: RNAseq in W22 pollen Rep1

value: pollen

value: WT

value: mature pollen


title: sBLISS_ctrl_siRNA_EV_rep2

value: ctrl siRNA + EV


title: TF ChIPseq of TU1A-YFP in bd1;Tu B73 ears IP Rep1

data_processing:
Adapter trimming with cutadapt
Mapping to each respective genome with bowtie2 (parameters:  --end-to-end --maxins 1500)
For Input, coverage tracks (bigwig) were created with deeptools bamCoverage
For IP, peaks were identified by calling peak with macs2 using the corresponding Input control. H3K4me1 broad peaks were called with parameter --broad, the other IPs narrow peaks were called with --call-summits.
For TF IP, tracks of log fold change enrichment of IP over Input were created with deeptools bamCompare (parameters: --scaleFactorsMethod "None" --normalizeUsing CPM --extendReads 300)
Assembly: B73 NAM; NC350 NAM; W22 v2; TIL11 v1.1
Supplementary files format and content: For Input: bigiwig file (coverage) for histone, logFC IP/Input for TFs.
Supplementary files format and content: For IP: list of identified peaks (macs2 narrowPeak or broadPeak format)

source_name: ears

growth_protocol: For collecting immature ears, maize inbreds were grown in the CSHL Uplands Farm field in the summer until they reached the appropriate stage. The plants were collected from the field, and 5-10mm primary and secondary ear primordia were dissected in the lab then frozen in LN2 and stored at -80°C. TIL11 plants were grown in CSHL Upland Farm field from September to early October to promote floral transition by natural short day conditions. Immature TIL11 ears at an equivalent development stage (with inflorescence meristems, spikelet pair meristems, spikelet meristems and floral meristems) were collected under a dissecting microscope, frozen in LN2 stored at -80°C. For endosperm samples, ears of field-grown plants were sib-pollinated and collected 15 DAP. Endosperm was dissected in the lab, frozen in LN2 and stored in -80°C. For root tips samples, seeds were germinated on wet paper towels in a Pyrex dish kept in the incubator at 26°C in continuous darkness. After 5 days, 1-3 mm root tips were cut off with a razor blade on ice, frozen in LN2 and stored at -80°C. For coleoptilar nodes samples, seeds were germinated in flats in a long day (8h dark/16h light) growth chamber, 27°C day and 24°C night, and light at 130 μmoles at the top flat. After 5 days, seedlings were unearthed and 5 mm sections around coleoptilar nodes were dissected on ice, frozen in LN2 and stored at -80°C. For TFs ChIPseq, TU1A-YFP (Han, Jackson, and Martienssen 2012), and GT1-YFP (Whipple et al. 2011) transgenic lines were introgressed into the bd1;Tunicate (bd1;Tu) double mutant background, which produces highly proliferative ears, to generate large amounts of ear tissue.

extract_protocol:
For histone ChIPseq, chromatin was extracted as previously described (Villar and Köhler 2010). Briefly, tissue was crosslinked with 1% formaldehyde, ground and sheared with Covaris ultrasonicator. Mixture of Dynabeads with proteins A and G (1:1) (Invitrogen) was used for the IP and DNA was purified using ChIP Clean-up and Concentrator kit (Zymo Research). For TFs ChIP-seq, chromatin was extracted as previously described (Xu et al. 2021).
Histone ChIPseq libraries were constructed using Ultra II DNA kit (NEB). TF ChIP-seq libraries were constructed with NEXTflex ChIPseq kit (PerkinElmer Applied Genomics)

value: ears

tag: antibody

value: GFP-Trap magnetic agarose (ChromoTek, gtma-20)


title: TF ChIPseq of TU1A-YFP in bd1;Tu B73 ears IP Rep2


title: TF ChIPseq of TU1A-YFP in bd1;Tu B73 ears Input Rep2

description: seq1 fastq files were done on NExtSeq500 PE150, seq2 and seq3 were sequenced on MiSeq PE75. All three runs were merged for analysis.


title: kuramochi_T20,replicate 2,ATAC-Seq

value: treated with 20uM of olaparib


title: EV(RBN)

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: prostate

growth_protocol: 22RV1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: prostate

value: 22RV1 cells

value: prostate cancer cells

value: the control group of overexpression of RBN by plasmids

value: transfection infection


title: kuramochi_T40,replicate 2,ATAC-Seq

value: Cell line

value: Kuramochi

value: Epithelial

value: treated with 40uM of olaparib


title: sBLISS_ctrl_siRNA_EV_rep1

value: luminal breast cancer


title: kuramochi_T40,replicate 1,ATAC-Seq


title: HA-RBN

value: the treat group of overexpression of RBN by plasmids


title: HA-RB(245-255)

value: the control group of overexpression of RB(245-255) by plasmids


title: HA-RB(245-255)_IgG


title: TF ChIPseq of GT1-YFP in bd1;Tu B73 ears IP Rep2


title: kuramochi_T10,replicate 2,ATAC-Seq

value: treated with 10uM of olaparib


title: kuramochi_T10,replicate 1,ATAC-Seq


title: TF ChIPseq of GT1-YFP in bd1;Tu B73 ears IP Rep1


title: TF ChIPseq of GT1-YFP in bd1;Tu B73 ears Input Rep1


title: TF ChIPseq of GT1-YFP in bd1;Tu B73 ears Input Rep2


title: kuramochi_T160,replicate 1,ATAC-Seq

value: treated with 160uM of olaparib


title: EV(245-255)_IgG


title: RB1_S1_IgG

value: the treat group of knockdown of RB1 by siRNA


title: Input for ChIPseq in W22 roots Rep2

value: root tips

value: WT


title: EV(245-255)

value: prostate


title: ChIPseq of H3K4me3 in W22 roots Rep2

value: H3K4me3 (Millipore, 07-473)


title: kuramochi_T5,replicate 2,ATAC-Seq

value: treated with 5uM of olaparib


title: Input for ChIPseq in W22 roots Rep1


title: kuramochi_C,replicate 2,ATAC-Seq

description: table containing consensus peaks across samples and read counts (C, T5 to T320,P10,P320), bigwig merged of the two C replicates

value: untreated


title: kuramochi_T5,replicate 1,ATAC-Seq


title: kuramochi_C,replicate 1,ATAC-Seq


title: RB1_NC_IgG

value: 22RV1 cells

value: prostate cancer cells

value: the control group of knockdown of RB1 by siRNA

value: transfection infection


title: TF ChIPseq of TU1A-YFP in bd1;Tu B73 ears Input Rep1

value: ears


title: kuramochi_T20,replicate 1,ATAC-Seq

value: Cell line

value: Kuramochi

value: Epithelial

value: treated with 20uM of olaparib


title: RB1_S1


title: ChIPseq of H3K4me3 in W22 roots Rep1


title: pc9_pool_C_to_T1.2_P1.2,scRNA-Seq

description: expression counts for all samples including untreated (C) and adapted cells from 8 nM to 1.2 uM of osimertinib plus persister cells treated with 1.2 uM of osimertinib. Sample ids are attached to cell barcode names (column names).

data_processing:
Raw reads were processed with the CellRanger v7.0.0 (10X genomics) pipeline using cellranger count command with default parameters and with the hg38/GRCh38 genome and Ensembl 93 transcriptome references. Sample demultiplexing was performed with the CellRanger v7.0.0 (--min-assignment-confidence 0.8) and the Fastq files and CMO IDs indicated in the config file according to the cell ranger 7.0 manual. For the A375 experiment, the correspondence between samples and CMO tags are: C: CMO301; T003: CMO302; T006: CMO303; T0125: CMO304; T0250: CMO305; T0500: CMO306; T1: CMO307; T2: CMO308 and T4: CMO309). For the PC9 experiment, the correspondence between samples and CMO tags are: C: CMO301; T0008: CMO302; T0016: CMO303; T0032: CMO304; T0075: CMO305; T0150: CMO306; T0300: CMO307; T0600: CMO308; T1.2: CMO309; P1.2: CMO310
Assembly: hg38/GRCh38
Supplementary files format and content: a375_all_C_to_T4.csv.gz, count expression matrix for A375 cells. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes, more than 700 umis expressed and less than average plus two standard deviations of umi counts. Rows are protein coding genes expressed in at least 1% of the cells.
Supplementary files format and content: pc9_all_C_to_T1.2_P1.2.csv.gz, count expression matrix for PC9 cells. Sample ids are attached to cell barcode names (column names). Cells were filtered based on expression of less than 20% of mitochondrial genes, more than 500 genes and more than 700 umis expressed and less than average plus two standard deviations of umi counts. Rows are protein coding genes expressed in at least 1% of the cells.

growth_protocol: PC9 cells were cultured in RPMI-1640 (ThermoFisher) with 10% Fetal Bovine Serum (FBS), 1% L-Glutamine 200 mM, 1% Penicillin and Streptomycin (10,000 U/mL, ThermoFisher). A375 cells were cultured in DMEM (ThermoFisher) supplemented with 10% FBS, 1% L-Glutamine and 1% Penicillin and Streptomycin.

extract_protocol:
Cells were trypsinized and single-cell suspensions were counted and pooled for cell tagging method using the 10X Genomics CellPlex kit Set A according to manufacturers protocol. The cell pool was loaded for droplet-based scRNA-Seq using the 10X Genomics Chromium platform according to the manufacturer's protocol.
Library preparation was performed using the 10X Genomics Chromium platform with the Chromium Single Cell Library & Gel Bead Kit v3.1 following the manufacturer’s instructions. For sample pooling, cell suspensions from each corresponding sample were labeled using the 10X Genomics 3’ CellPlex kit Set A according to the manufacturer’s instructions. Cells were pooled in equal amounts and loaded in the 10X Genomics Chromium Controller. For A375 experiment, the correspondence between samples and CMO tags are: C: CMO301; T003: CMO302; T006: CMO303; T0125: CMO304; T0250: CMO305; T0500: CMO306; T1: CMO307; T2: CMO308 and T4: CMO309). For the PC9 experiment, the correspondence between samples and CMO tags are: C: CMO301; T0008: CMO302; T0016: CMO303; T0032: CMO304; T0075: CMO305; T0150: CMO306; T0300: CMO307; T0600: CMO308; T1.2: CMO309; P1.2: CMO310

treatment_protocol: A375 cells were treated in dose escalation from 30 nM to 4 uM of dabrafenib, generating populations resistant to 30 nM, 60 nM, 125 nM, 250 nM, 500 nM, 1 uM, 2 uM and 4 uM (T003, T006, T0125, T0250, T0500, T1, T2 and T4) plus untreated control (C). PC9 cells were treated in dose escalation from 8nM to 1.2 uM of osimertinib, generating resistant populations to 8 nM, 16 nM, 32 nM, 75 nM, 150 nM, 300 nM, 600 nM and 1.2 uM  (T0008, T0016, T0032, T0075, T0150, T0300, T0600, T1.2) plus untreated control (C). A population of persister cells was generated by acute exposure to 1.2 uM (P1.2)

value: Epithelial, lung adenocarcinoma

value: EGFR-del

value: untreated and resistant cells from 8 nM to 1.2 uM of osimertinib plus persister cells treated with 1.2 uM of osimertinib for 9 days (P1.2)


title: ChIPseq of H3K4me1 in W22 roots Rep1

value: root tips

value: WT

value: H3K4me1 (Abcam, ab8895)


title: ChIPseq of H3K4me1 in W22 roots Rep2